Mr Morrison says he will personally apply a so-called "national interest" test for permanent protection applications from people who arrive without a visa.
It comes two weeks after the High Court struck down the Government's attempt to cap the number of protection visas for some refugees.
Greens senator Sarah Hanson-Young has told the ABC the Minister is defying, not only the will of the Parliament - but the ruling of the High Court.
"This is clearly an act of desperation by Mr Morrison. It is him, his department, acting in a way that seems to be not just above the law, but above the parliament."
The reasons for refusing a protection visa under the national interest test include not wanting to "reward people who arrive illegally".
Other reasons cited include: ensuring the communtiy's confidence is not "eroded" and removing a "product for people smuglers to market".
The plan was announced in a letter to lawyers acting for a teenager who successfully challenged the the government's protection visa cap.
The letter said the Minister has refused protection visa status for the teenager, saying it would not be in the national interest. The lawyers have been given 28 days to provide another reason why a protection visa should be granted.
One of the lawyers, David Manne, said the legal team has gone back to the court and awaits a response over the next fortnight.
He warns if the move fails then a High Court challenge to the national interest test is possible.
"If that decision is a refusal, we will be challenging the refusal on national interest grounds in the High Court," he told the ABC.
Mr Manne said he finds it strange that the government had not invoked the national interest test for protection visa applications in the past.
"One thing is crucial here. If the government got its way on this somehow and the national interest was applied - as it hasn't been in the past - we would be looking at the consequence of someone being found to be a refugee in this country...but then potentially consigned to indefinite limbo in the community or in detention."
